diff --git a/src/pyscenic/export.py b/src/pyscenic/export.py index 11d481d..422b76a 100644 --- a/src/pyscenic/export.py +++ b/src/pyscenic/export.py @@ -45,10 +45,12 @@ def export2loom(ex_mtx: pd.DataFrame, regulons: List[Regulon], out_fname: str, :param regulons: A list of Regulons. :param cell_annotations: A dictionary that maps a cell ID to its corresponding cell type annotation. :param out_fname: The name of the file to create. - :param tree_structure: A sequence of strings that defines the category tree structure. + :param tree_structure: A sequence of strings that defines the category tree structure. Needs to be a sequence of strings with three elements. :param title: The title for this loom file. If None than the basename of the filename is used as the title. :param nomenclature: The name of the genome. :param num_workers: The number of cores to use for AUCell regulon enrichment. + :param embeddings: A dictionary that maps the name of an embedding to its representation as a pandas DataFrame with two columns: the first + column is the first component of the projection for each cell followed by the second. The first mapping is the default embedding (use `collections.OrderedDict` to enforce this). :param compress: compress metadata (only when using SCope). """ # Information on the general loom file format: http://linnarssonlab.org/loompy/format/index.html